LiftOver, HGVS, dbSNP and other variant converter
Information about converter and liftover
Usage in python is described in pandas chapter.
Until there is no better documentation, visit the OpenAPI documentation here:
For liftover:
https://api.genebe.net/cloud/gb-api-doc/swagger-ui/index.html#/liftover-public-controller/lift_1
For HGVS and other converter:
Example GET
Example of converting dbSNP rs11 to VCF-like position:
# convert dbSNP id:
curl -X 'GET' \
'https://api.genebe.net/cloud/api-public/v1/convert?id=rs11&genome=hg38' \
-H 'accept: */*'
[
{
"variants": [
{
"genome": "hg38",
"chr": "7",
"pos": 11324574,
"ref": "C",
"alt": "T"
}
]
}
]
Examples
Example of converting HGVS NM_018136.4:c.567_569del to VCF-like position:
# convert dbSNP id:
curl -X 'GET' \
'https://api.genebe.net/cloud/api-public/v1/convert?id=NM_018136.4:c.567_569del&genome=hg38' \
-H 'accept: */*'
[
{
"variants": [
{
"genome": "hg38",
"chr": "1",
"pos": 197143682,
"ref": "GCTC",
"alt": "G"
}
]
}
]
Example of converting deletion 22-28695869-G- to VCF-like position:
# convert dbSNP id:
curl -X 'GET' \
'https://api.genebe.net/cloud/api-public/v1/convert?id=22-28695869-G-&genome=hg38' \
-H 'accept: */*'
[
{
"variants": [
{
"genome": "hg38",
"chr": "22",
"pos": 28695868,
"ref": "AG",
"alt": "A"
}
]
}
]
Endpoint should also work well for p. HGVS or even query like AGT M259T. Be careful though, this conversion may not always work as exptected.
curl -X 'GET' \
'https://api.genebe.net/cloud/api-public/v1/convert?id=AGT%20M259T&genome=hg38' \
-H 'accept: */*'
[
{
"variants": [
{
"genome": "hg38",
"chr": "1",
"pos": 230710048,
"ref": "A",
"alt": "G"
}
]
}
]